. "13 Gene Genealogies and Population Variation in Plants." Variation and Evolution in Plants and Microorganisms: Toward a New Synthesis 50 Years after Stebbins. Washington, DC: The National Academies Press, 2000.
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Variation and Evolution in Plants and Microorganisms: TOWARD A NEW SYNTHESIS 50 YEARS AFTER STEBBINS
of these haplotypes near the tips of the gene tree also favors this explanation over shared ancestral polymorphisms; tip haplotypes are likely to be younger than interior haplotypes (Castelloe and Templeton, 1994) and therefore would be less likely to represent ancestral variation. The third shared haplotype (M) is also a tip haplotype. However, this haplotype is common in M. pruinosa and is found in a single flabellifolia population approximately 1,000 km west of the current range of M. pruinosa. Although clearly not the result of contemporary gene flow, this pattern could possibly have arisen through hybridization in the recent past. Palynological data indicate that during the last glacial maximum (<18,000 years B.P.), cerrado vegetation expanded into areas along the southern border of the Amazon basin that are presently rainforest (reviewed in Burnham and Graham, 1999). Thus, hybridizing pruinosa populations could have existed in this region as recently as 11,000 years B.P.
Haplotypes on the G3pdh tree are not clustered by species (Fig. 4). Because flabellifolia and pruinosa are closely related taxa within a recently radiated genus, they would not necessarily be expected to have reached a pattern of reciprocal monophyly with respect to G3pdh haplotypes (Fig. 2). The phylogeographic structure within each species is also complex. However, although there is no simple concordance between the geographical distributions of haplotypes and their genealogical relationships, contingency analyses (Posada et al., 1999) reveal that nested clades within the gene tree are geographically structured. Thus, the phylogeographic structure reflects more than just the random sorting of ancestral polymorphisms among populations. Detailed phylogeographic analysis (Templeton et al., 1995) and the analysis of DNA sequence data from two additional nuclear genes (K.M.O., unpublished data) will be useful in elucidating the historical processes that have led to the current phylogeographic structure in this study system.
Gene genealogies have lead to several important insights into plant evolution and have the potential for far greater contributions. Many of the processes that affect the evolution of plant populations, such as selection, isolation, size fluctuations, and gene flow, are amenable to genealogical analysis. In particular, the use of genealogies within the framework of coalescence theory will allow us to understand in greater detail the role of historical fluctuations in population size, colonization, and range expansion. Although the large-scale metapopulation structure of many plants is clearly documented, there are relatively few studies of the genetic dynamics of this structure: colonization and establishment of subpopula-